The gut microbiota reacts to lifestyle, but the media sometimes exaggerate the size of this reaction. Some factors change its composition in a measurable way, some only in certain studies, and for many we do not know what is the cause and what is the effect. Below, we describe these factors and show what data each statement is based on.
What dysbiosis is and why people overuse this term
The word “dysbiosis” often appears in popular texts, usually to describe a disturbed microbiota. But there is no widely accepted definition of this state and no threshold values to identify it.
To find a difference from normal, you need a point of reference, and there is no agreed pattern of a normal microbiota. Also, healthy people differ a lot.
Read more: Gut microbiota – how it develops and what shapes it throughout life
The scientific literature uses the term to describe a difference in composition between the groups that a study compares. It is not a clinical diagnosis.
So below, we describe factors linked to changes in the composition of the microbiota, not diseases.
A low-fibre and highly processed diet
Diet is the best documented factor, because it provides substrates, that is the material that microorganisms process.
Intervention studies are studies where researchers change one factor on purpose. In these studies, researchers saw changes in composition after people moved to a diet with a different amount of fibre. The changes were sometimes fast, but also temporary: when people went back to their earlier diet, the composition moved back towards its starting state.
In this context, studies describe highly processed diets by what they lack: components that are not digested in the upper part of the digestive tract. Much of the research on individual food additives uses in vitro or animal models, so conclusions for humans need separate studies.
The role of fibre
Dietary fibre and resistant starch reach the large intestine unchanged, and they are material for fermentation. Its products include short-chain fatty acids, which microbiota studies often measure.
Not every type of fibre ferments in the same way. Soluble fibre ferments more easily, and some types, for example cellulose, are processed poorly.
Read more: Dietary fibre – how much we really eat and how much institutions recommend
Observational studies have also described a link between the variety of plant foods in the diet and the variety of the microbiota. These are correlations, not proof of cause and effect.
Antibiotics and other medicines
The most important point: only a doctor makes decisions about treatment. Do not stop, change or shorten treatment because of information about the effect of medicines on the microbiota. If you have doubts, talk to a doctor or pharmacist.
Here, antibiotics are the best documented factor, because by definition they act on microorganisms. After treatment, studies observe changes in the variety and proportions of bacterial groups. The speed of return to the state before treatment differs between people.
Read more: The microbiota after antibiotic treatment – what research says and what to ask your doctor
This does not mean that you should avoid antibiotic treatment. It is a treatment for specific medical reasons, and a doctor makes the decision after weighing the benefits and risks in each situation.
Research also covers medicines other than antibacterial ones. In a screening study of more than a thousand medicines, about a quarter of the medicines targeting human cells stopped the growth of at least one gut strain in the laboratory. Studies with people are needed to show what these observations mean in clinical practice (Maier et al., 2018). A doctor decides whether to continue or change treatment.
Chronic stress and the gut-brain axis
The term “gut-brain axis” describes two-way communication between the digestive tract and the nervous system, through nerve, hormone and immune pathways. It is an area of research, not a fully described mechanism.
Chronic stress affects how the digestive tract works: it changes movement, secretion and blood flow. The effect on the composition of the microbiota has been studied mainly in animal models, with stress protocols that cannot be repeated in humans.
Studies with people are mostly observational and do not show the direction of the link. Stress may affect the microbiota, but other factors may also play a role, for example changes in diet and daily rhythm.
Lack of sleep and shift work
The daily (circadian) rhythm does not only apply to the host. Studies have described daily changes in the composition and activity of the microbiota, linked to mealtimes.
Shift work and lack of sleep disturb both the sleep rhythm and mealtimes, so it is hard to separate these effects. Some data comes from animal models, and some from small studies in humans.
A careful conclusion: regular mealtimes and sleep are an important variable in these studies, but the size of their effect in humans is not well defined.
Alcohol and smoking
The effect of alcohol on the digestive tract is described separately from the microbiota. It affects, among other things, the mucous membrane and the liver. Changes in the composition of the microbiota have been described with long-term drinking of large amounts.
Smoking is sometimes named among the factors linked to the composition of the microbiota, although most of the data comes from observational studies.
The same point applies in both cases: people who drink and smoke also differ from others in their diet and physical activity. This makes it hard to link the differences to one factor.
What we do not know about these links
| Factor | Main source of data | What we can say with care |
|---|---|---|
| Diet and fibre | Intervention studies in humans | A change in fibre intake is linked to a change in composition, often temporary |
| Antibiotics | Studies in humans, clinical observations | Changes in composition after treatment are well documented, the speed of return is individual |
| Other medicines | Laboratory studies, a few clinical studies | Early observations that need confirmation in humans |
| Stress | Animal models, observational studies in humans | Studies describe these things happening together, the direction of the link is not clear |
| Sleep and shift work | Animal models, small studies in humans | Meal and sleep rhythm is an important variable, the size of its effect is not defined |
| Alcohol and tobacco | Mainly observational studies | Differences in composition are described, but hard to link to one factor |
The problem of correlation and cause
Most media reports about the microbiota are based on observational studies. They show that a certain composition happens together with a certain condition, but they do not show which came first.
There are three possible explanations for the same observation: a factor affects the microbiota, the microbiota affects the observed condition, or both come from a third factor that the study did not include.
There are also limits in the methods. Researchers usually study the composition in a stool sample, which mainly describes the last part of the gut, and the result depends on how the sample is collected and analysed. There are also no reference values for an individual person.
So the statement “people with feature X had a different microbiota” does not mean that feature X damages the microbiota or that changing it will bring back that composition.
What you can really do
The points below are general advice about lifestyle and diet, in line with common rules of healthy eating. They are not advice to “fix” the microbiota, because current knowledge does not allow such advice.
- Eat fibre regularly from different sources. Vegetables, fruit, wholegrain products, pulses and nuts.
- Eat a variety of plant foods. More different plant products each week give a wider set of substrates.
- Fermented products as part of your diet. Pickles and fermented dairy products have long been part of traditional diets. Read more: Fermented food in Polish cooking – pickles, sour starters, kefir
- Regular mealtimes and sleep. These are the variables that appear most often in studies on the daily rhythm.
- Limit alcohol. This advice applies whatever the context of the microbiota.
- Physical activity that suits your abilities. This is part of general health advice.
- Take antibiotics only as your doctor advises. A doctor decides when to start, change and stop treatment.
If you have digestive problems that do not go away, see a doctor.
Summary
The composition of the microbiota changes with diet, medicines, daily rhythm, alcohol and tobacco, but knowledge about the size and duration of these changes is uneven. The effect of fibre intake and antibiotics is the best documented, and the effect of stress and sleep in humans is the least documented.
People overuse the term dysbiosis, because there is no agreed definition and there are no reference values for an individual result.
A large part of the reports comes from observational studies and animal models, so they do not prove cause and effect. In practice, this leads to advice that is part of a healthy lifestyle anyway: a varied diet with enough fibre, a regular daily rhythm, less alcohol and using medicines as your doctor advises.
FAQ
Does one week of a poorer diet destroy the microbiota?
Intervention studies show that changes in diet are linked to changes in the composition of the microbiota, but these changes can be temporary. The word “destroy” does not describe these observations correctly.
Does the microbiota return to its state before treatment after antibiotics?
Studies have described a gradual return towards the starting state, although the speed and degree differ between people. Take antibiotics only as your doctor advises. The doctor decides how the treatment goes.
Does stress really affect the gut?
The effect of stress on how the digestive tract works is described. It affects, among other things, movement and secretion. The effect on the composition of the microbiota itself has been studied mainly in animal models. Data from humans is observational, so it does not show the direction of the link.
Is it worth doing a microbiota test to check for damage?
Such a result is hard to interpret, because there are no widely accepted reference values for an individual person, and the result describes the state of the sample at the moment of sampling. If you have problems that do not go away, talk to a doctor.
Sources
- Koh A., De Vadder F., Kovatcheva-Datchary P., Bäckhed F., From dietary fiber to host physiology: short-chain fatty acids as key bacterial metabolites, Cell, 2016, vol. 165, no. 6, pp. 1332-1345.
- Gibson G.R., Hutkins R., Sanders M.E. et al., Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics, Nature Reviews Gastroenterology & Hepatology, 2017, vol. 14, no. 8, pp. 491-502.
- Marco M.L., Sanders M.E., Gänzle M. et al., The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods, Nature Reviews Gastroenterology & Hepatology, 2021, vol. 18, no. 3, pp. 196-208.
- Berg G., Rybakova D., Fischer D. et al., Microbiome definition re-visited: old concepts and new challenges, Microbiome, 2020, vol. 8, no. 103.
- Commission Regulation (EU) No 432/2012 of 16 May 2012 establishing a list of permitted health claims made on foods, other than those referring to the reduction of disease risk and to children’s development and health.
- National Antibiotic Protection Programme (Poland), educational materials and recommendations on the rational use of antibiotics, https://antybiotyki.edu.pl
- Maier L., Pruteanu M., Kuhn M. et al., Extensive impact of non-antibiotic drugs on human gut bacteria, Nature, 2018, vol. 555, no. 7698, pp. 623-628.